I don't think this is a matter of assumption or personal preference. In "By Any Other Name" Spock stated that the Enterprise is "propelled by matter-antimatter reactors" (i.e. more than one), there are several references to antimatter pods in the warp nacelles and "That Which Survives" suggests there is one that can be jettisoned should the need arise (given the episode's context apparently in the engineering hull).

blssdwlf compiled most of the corresponding dialogue quotes in his WIP Enterprise thread which I personally found most inspiring and eye-opening.

Sure it is! People have opinions regardless of the presence or absence of evidence. This is like asking if people believe in the existence of gods, human-triggered global warming, natural selection/evolution, the tooth fairy, honor among thieves or politicians, and the worldwide communist conspiracy. People have opinions about the location of the M/AM reaction, despite or because of the evidence, and I'd like to know what they think.

I believe that in TOS, the initial thought was that the nacelles were both power and propulsion units, akin to the aviation model with which Mr. Jefferies and Gene were accustomed. Indeed, I'd say "antimatter pods = warp nacelles." However, I think this may have changed, even during the show.

Taking the universe in whole, I'd posit that there's some sort of reactor in the secondary hull, probably a multi-chamber/reactor system, and then some sort of plasma accelerator system system in the nacelles themselves... maybe some kind of final stage reactors?

Sure it is! People have opinions regardless of the presence or absence of evidence.

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No offense, but in the presence of evidence we are enabled to draw logical conclusions and do not need to rely on opinion, belief, assumption or preference.

In the absence of evidence speculation is warranted and I can immediately think of the in-universe size of the Excelsior, the function of the numbered openings at Reliant's stern, the age of the Oberth Class and other topics.

Anyway, here are the relevant TOS quotes regarding the issue. Where I reserve doubt is the function of dilithium crystals, but the location of the antimatter pods (and reactors) aboard the TOS Enterprise is made abundantly clear, IMO.

I would also like to add that Spock located the alien entity in "Day of the Dove" near "reactor number three".

Robert Comsol, don't be a wet blanket! If you object to this thread and the whole idea of this poll, then just ignore it. Regardless of what you believe people should conclude, I know for a fact that people have different opinions about this issue. Let people express themselves. Please don't try to influence their opinions; I've requested that people, including you, not do that. OK?

My vote goes for "the creators of the show never cared and thus never knew", the one thing for which there is rock-solid evidence.

Oh, wait, that has been left out of the choices for some reason...

Okay, it's the "combination" thing, then. Clearly, the flow of antimatter flow takes place in the secondary hull ("That Which Survives"), in addition to potentially happening elsewhere. If the antimatter pods are in the nacelles, what business would the fuel have in the secondary hull unless it went there for rest, recreation and reaction?

Basically, the one problem we face with the TOS ship is finding a part of it that does not have antimatter within! Even the saucer seems to have some, as per "Errand of Mercy".

. . .In the absence of evidence speculation is warranted and I can immediately think of the in-universe size of the Excelsior, the function of the numbered openings at Reliant's stern, the age of the Oberth Class and other topics. . .

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Which is completely irrelevant, given the conditions presented in the first sentence of the original post:

Without referring to anything that came after TOS (no retconning!), where do you think the matter/antimatter reaction took place on TOS USS Enterprise: in the nacelles or in an in-hull reactor?

LET ME STRESS: TOS ENTERPRISE!!!

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It take place in the intermix chamber, which itself is located in the engineering hull, just behind main engineering.
Later it was move below main engineering in the middle with the top part of it extending into engineering itself.

As I understand it, Matt Jeffries intended the reactors to be in the nacelles, and TMP was supposed to be a big deal with the refit moving them. So I prefer TOS reactors in the nacelles, with the move to a single reactor in the hull as the upgrade that set the pattern for the future.
It also allows the technology change to affect ship design. A TOS Chandley might have had room for everything it was supposed to if the reactors are in the nacelles. Moving the reactor into the hull makes it way too cramped. Same with Saladins, Loknars, etc. This goes along with the ships getting bigger - part of the reason for the larger saucer on the refit E, by this thinking, is to recoup space lost to the reactor, not to balance the appearance. It also goes a ways towards explaining the Indomitable, with it's stretched Connie-refit secondary hull. To be a battleship, it needed a larger reactor to allow more weapons, shield, and maneuvering power, and needed not to take space out of the primary hull, so they stretched the secondary hull. I really like the Indomitable, especially the fan variants that switch back to an Enterprise saucer, but I've never really liked the idea of it as a battleship.
I can see the Excelsior being able to fill that role initially, until everyone catches up, even though it's supposed to be the new generation of heavy cruiser, but AFAIAC, the Federation refit is a better BB than Indomitable. But considering the switch from nacelles to secondary hulls gives an in-universe explanation for why it was intended as such. In my trek verse, it was introduced as a battle cruiser, not a battleship, and reclassified as a CH after Excelsior came online.
Also, the TOS ship was capable of warp 6/8, the refit 8/12. Part of that was, IMO, the better engines, and part was the much bigger reactor providing more power to those new engines, since the Kelvans got the TOS E up to warp 14.
And then, finally, I like to think the later recalibration of the warp scale became necessary as the new liner-intermix style reactors evolved and got bigger, allowing engines to go faster by accessing deeper layers of subspace.

Having gone through all the scripts using key word search terms, I decided that they were in the nacelles. That said, there were clearly other forms of reactors for power and batteries throughout the ship. I have no problem with that.

I also have no issue with other Starfleet ships have the main warp power reactors being located in the main hull(s) as per design requirements. But I'm completely convinced that Starship Class (Constitution Class) ships, i.e. TOS Enterprise and her sisters, all had their main warp reactors contained within the nacelles.

A little off topic, I even really think TMP's main reactors should be a more efficient stream lined version of TOS's systems. Where the power from the nacelle reactors are the sole source (Other than backup batteries), and engineering is where that energy is converted and shunted to the rest of the ship. Minus other reactors like in TOS. Then by the end of the 2200's we see a conversion to a centralized warp core that are due to more efficient and powerful controls for m/arc energy containment. Pre-TOS had a centralized warp core because they weren't as powerful, and required more hands on maintenance.

My vote was for in the nacelles. This way the reactors would be ajacent to the the warp engines which consume the majority of the reactors output. A small amount of the reactors output would be transferred down to the engineering hull to be used by the rest of the ship's systems, either directly as plasma or converted into electricity.